[gmx-users] NMA for a group

[Bert de Groot]

David van der Spoel wrote:
> Christian Seifert wrote:
>> Hi.
>>
>> Perhaps, I made a mistake in describing my problem. I can not believe,
>> that no one ever tried this before.
>>
>> I have a phosphate in water and want to calculate the hessian just for
>> the phosphate. How do I do that?
> 
> there is a contradiction here in that you say the phosphate is in water
> and you want to do the NMA for just the phosphate. Something like that
> might work with a continuum solvent but I don't know how you would do it
> with explicit solvent.


right. one way to include water and still have a manageable system size is to
work with a small droplet of explicit water.


Bert

______________________________________
Bert de Groot, PhD

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302
http://www.mpibpc.mpg.de/groups/de_groot